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{{Coexpression_clusters
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|full_id=C1166_cerebellum_occipital_middle_pineal_parietal_thalamus_acute
|id=C1166
}}

Latest revision as of 11:39, 17 September 2013


Full id: C1166_cerebellum_occipital_middle_pineal_parietal_thalamus_acute



Phase1 CAGE Peaks

Hg19::chr12:132640129..132640150,+p@chr12:132640129..132640150
+
Hg19::chr1:7552597..7552608,+p@chr1:7552597..7552608
+
Hg19::chr3:129089024..129089057,-p@chr3:129089024..129089057
-
Hg19::chr3:129089229..129089276,-p@chr3:129089229..129089276
-
Hg19::chr3:129089385..129089423,-p@chr3:129089385..129089423
-
Hg19::chr3:129089547..129089586,-p@chr3:129089547..129089586
-
Hg19::chr3:129089810..129089831,-p@chr3:129089810..129089831
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube1.88e-2856
neural rod1.88e-2856
future spinal cord1.88e-2856
neural keel1.88e-2856
regional part of nervous system7.96e-2853
regional part of brain7.96e-2853
brain8.77e-2668
future brain8.77e-2668
central nervous system1.07e-2481
regional part of forebrain4.65e-2441
forebrain4.65e-2441
anterior neural tube4.65e-2441
future forebrain4.65e-2441
nervous system8.10e-2489
adult organism4.05e-22114
brain grey matter3.58e-2034
gray matter3.58e-2034
telencephalon5.20e-2034
neurectoderm8.00e-1986
regional part of telencephalon1.18e-1832
cerebral hemisphere1.95e-1832
neural plate3.01e-1782
presumptive neural plate3.01e-1782
regional part of cerebral cortex1.08e-1522
neocortex4.63e-1420
cerebral cortex8.72e-1425
pallium8.72e-1425
pre-chordal neural plate1.11e-1361
organ system subdivision1.79e-11223
ecto-epithelium2.16e-11104
ectoderm-derived structure1.14e-09171
ectoderm1.14e-09171
presumptive ectoderm1.14e-09171
neural nucleus5.00e-089
nucleus of brain5.00e-089
structure with developmental contribution from neural crest5.86e-08132
basal ganglion6.87e-089
nuclear complex of neuraxis6.87e-089
aggregate regional part of brain6.87e-089
collection of basal ganglia6.87e-089
cerebral subcortex6.87e-089
Disease
Ontology termp-valuen
cell type cancer7.10e-09143
cancer1.96e-08235
disease of cellular proliferation6.93e-08239


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0462779
MA0004.11.25543
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.14.25487
MA0043.10.973609
MA0046.10.962263
MA0048.11.25271
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.11.04727
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.12.88764
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.1130.337
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.11.63168
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.162729
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.22.53691
MA0137.20.95459
MA0104.20.636673
MA0047.20.636643
MA0112.20.556641
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.780982
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NR2C2#7182418.63692051728052.86862168958321e-050.000604145958133457
SUZ12#23512428.63758909203595.27895839013948e-060.000161348883613631



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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